[clade-i] ignore colors for certain categories

We don't want an ordering for division & location in the clade-I builds
as these are constantly changing and we want to avoid auspice using
greys for demes

phylogenetic/defaults/clade-i/config.yaml

@@ -57,3 +57,6 @@ mask:
   from_beginning: 800
   from_end: 6422
   maskfile: "defaults/mask.bed"
+
+colors:
+  ignore_categories: "division location"

phylogenetic/rules/export.smk

@@ -48,12 +48,17 @@ rule colors:
         metadata=build_dir + "/{build_name}/metadata.tsv",
     output:
         colors=build_dir + "/{build_name}/colors.tsv",
+    params:
+        ignore_categories=lambda w: config.get("colors", {}).get(
+            "ignore_categories", ""
+        ),
     shell:
-        """
+        r"""
         python3 scripts/assign-colors.py \
             --ordering {input.ordering} \
             --color-schemes {input.color_schemes} \
             --output {output.colors} \
+            --ignore-categories {params.ignore_categories} \
             --metadata {input.metadata} 2>&1
         """
 

phylogenetic/scripts/assign-colors.py

@@ -16,6 +16,8 @@
     parser.add_argument('--color-schemes', type=str, required=True, help="input color schemes file")
     parser.add_argument('--metadata', type=str, help="if provided, restrict colors to only those found in metadata")
     parser.add_argument('--output', type=str, required=True, help="output colors tsv")
+    parser.add_argument('--ignore-categories', type=str, required=False, nargs='*',
+                        help="Do not create colors for these categories")
     args = parser.parse_args()
 
     assignment = {}
@@ -25,6 +27,8 @@
             if len(array) == 2:
                 name = array[0]
                 trait = array[1]
+                if name in args.ignore_categories:
+                    continue
                 if name not in assignment:
                     assignment[name] = [trait]
                 else: